This experiment was carried out on plastic pots ($40cm{ imes}25cm{ imes}30cm$) filled with sand soil at greenhouse using two soybean cultivars with small seed; one was Pungsannamulkong (PSNK) recognized as a tolerant cultivar against excessive water stress and the other one was Sobaeknamulkong (SBNK) recognized as a susceptible cultivar. Seed was sown with 30 plants of 2 hills, and the amount of applied fertilizer was N; 3.0 g, P; 3.0 g, and K; 3.4 g per $m^2$ with all basal fertilizations. Plants were grown under photoperiod of natural light with day temperature of $31{pm}5^{circ}C$ and night temperature of $22{pm}1^{circ}C$. The flooding treatment was done for 3, 5, 7 and 10 days by filling pots with tap water up to 1 cm above the level of the soil surface when plants were 2 days after emerging. Nitrogen uptake by leaves of soybeans decreased significantly by the flooding after 6 days. This significant reduction of N uptake by flooding was evidently recognized from the chlorosis of leaves. The dry matter of flooded soybean seedlings significantly decreased compared to non-flooded soybean seedlings at 10 days. The dry matter of roots also showed similar result of the shoot. Shoots had more N reduction than roots under the flooding. This N reduction was more pronounce in SBNK than in PSNK. Chlorophyll content of flooded soybeans showed decreasing or non-increasing tendency, and the reduction of chlorophyll content was more in SBNK than in PSNK from the flooding stress. Nitrate content of soybean seedlings with flooding stress showed decreasing tendency in shoot and root parts. Ammonium content, however, was higher in flooding stress compared to the non-flooding. Flooding caused a remarkable change in the AA (amino acid) composition and TAA (total amino acid) concentration in the leaves of soybean seedlings.